{"files"=>["https://ndownloader.figshare.com/files/510433"], "description"=>"<p>(A) Alignment of a representative subset of the secretin sequences used in this study to demonstrate sequence conservation (darker to lighter shades of green represent higher to lower levels of sequence conservation). Accession numbers for all secretins investigated in this study are given in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003117#ppat.1003117.s007\" target=\"_blank\">Table S2</a>. (B) S-domain sequences from the secretins were subject to CLANS analysis <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003117#ppat.1003117-Frickey1\" target=\"_blank\">[29]</a>. The position corresponding to each S-domain sequence from the <i>Vibrio</i>-type EpsD and GspD proteins is represented by red dots, ExeD by orange dots and the group circled in red. The position corresponding to each sequence from the <i>Klebsiella</i>-type PulD, OutD, EtpD and GspD proteins is colour-coded in blue. The connections shown represent an E-value cut-off of 1e−10. (C) <i>E. coli</i> BL21(DE3)(Δ<i>gspD</i>,Δ<i>aspS</i>) complemented with either pETDuet (GspD-C<sub>4</sub>+AspS) or pETDuet (GspDΔS-C<sub>4</sub>+AspS) were cultured to an OD<sub>600</sub> of ∼0.6 and IPTG was added to the culture (0.1 mM, final concentration). At the indicated time-point cell extracts were prepared from the cultures and incubated with a modified sample buffer containing Lumio reagent, analysed by SDS-PAGE and imaged by fluorimetry. (D) Size-exclusion chromatography profiles of the purified AspS (red), the purified MBP-S-domain fusion (green) and the complex of AspS and MBP-S-domain fusion (blue) on a Superdex200 column. An SDS-PAGE gel of the peak fractions of AspS-MBP-S-domain complex shows an approximately stoichiometric ratio of the two proteins. A280, absorbance at 280 nm; mAU, milli absorbance units. <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003117#ppat.1003117.s005\" target=\"_blank\">Figure S5</a> shows the results of the control experiment, where AspS and MBP without S-domain do not interact.</p>", "links"=>[], "tags"=>["s-domains", "secretins", "diagnostic"], "article_id"=>180912, "categories"=>["Microbiology", "Biochemistry"], "users"=>["Rhys A. Dunstan", "Eva Heinz", "Lakshmi C. Wijeyewickrema", "Robert N. Pike", "Anthony W. Purcell", "Timothy J. Evans", "Judyta Praszkier", "Roy M. Robins-Browne", "Richard A. Strugnell", "Konstantin V. Korotkov", "Trevor Lithgow"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003117.g005", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_S_domains_of_i_Vibrio_i_type_secretins_have_diagnostic_sequence_features_/180912", "title"=>"The S-domains of <i>Vibrio</i>-type secretins have diagnostic sequence features.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-10 00:15:12"}

{"files"=>["https://ndownloader.figshare.com/files/510198"], "description"=>"<p>(A) The expression cassette in pETDuet plasmids GspD-C<sub>4</sub>, GspD-C<sub>4</sub>+AspS and GspD-C<sub>4</sub>+YacC are represented diagrammatically. The pETDuet-1 vector (Novagen) has two multi-cloning sites (MCS) represented as black squares, and cloning into the NcoI and NdeI sites is optimal with respect to the ribosome-binding sites: NcoI and HindIII sites were used to clone the open-reading frame corresponding to GspD-C<sub>4</sub>; NdeI and XhoI sites were used to clone the open-reading frame corresponding to AspS and YacC. The T7 terminator sequence (T) in the plasmid is represented by a black triangle. (B) <i>E. coli</i> BL21(DE3)(Δ<i>gspD</i>,Δ<i>aspS</i>) complemented with pETDuet (GspD-C<sub>4</sub>) or pETDuet (GspD-C<sub>4</sub>+AspS) were cultured to an OD<sub>600</sub> of ∼0.6 and IPTG was added to the culture (0.1 mM, final concentration). At the indicated time-point cell extracts were prepared from the cultures using Lumio analysed by SDS-PAGE and imaged by fluorimetry. (C) The strains described above were cultured to an OD<sub>600</sub>∼1, extracted and then fractionated by sucrose density centrifugation. Replicate samples were analysed by SDS-PAGE for detection of GspD multimers with Lumio reagent and immunoblotting for BamA and F<sub>1</sub>β.</p>", "links"=>[], "tags"=>["targeting", "gspd", "membrane", "depends"], "article_id"=>180686, "categories"=>["Microbiology", "Biochemistry"], "users"=>["Rhys A. Dunstan", "Eva Heinz", "Lakshmi C. Wijeyewickrema", "Robert N. Pike", "Anthony W. Purcell", "Timothy J. Evans", "Judyta Praszkier", "Roy M. Robins-Browne", "Richard A. Strugnell", "Konstantin V. Korotkov", "Trevor Lithgow"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003117.g003", "stats"=>{"downloads"=>1, "page_views"=>46, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Subcellular_targeting_of_GspD_to_the_outer_membrane_depends_on_AspS_/180686", "title"=>"Subcellular targeting of GspD to the outer membrane depends on AspS.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-10 00:11:26"}

{"files"=>["https://ndownloader.figshare.com/files/277707", "https://ndownloader.figshare.com/files/277758", "https://ndownloader.figshare.com/files/277812", "https://ndownloader.figshare.com/files/277887", "https://ndownloader.figshare.com/files/277962", "https://ndownloader.figshare.com/files/278033", "https://ndownloader.figshare.com/files/278108", "https://ndownloader.figshare.com/files/278197", "https://ndownloader.figshare.com/files/278293"], "description"=>"<div><p>The Type II Secretion System (T2SS) is a molecular machine that drives the secretion of fully-folded protein substrates across the bacterial outer membrane. A key element in the machinery is the secretin: an integral, multimeric outer membrane protein that forms the secretion pore. We show that three distinct forms of T2SSs can be distinguished based on the sequence characteristics of their secretin pores. Detailed comparative analysis of two of these, the <em>Klebsiella</em>-type and <em>Vibrio</em>-type, showed them to be further distinguished by the pilotin that mediates their transport and assembly into the outer membrane. We have determined the crystal structure of the novel pilotin AspS from <em>Vibrio cholerae</em>, demonstrating convergent evolution wherein AspS is functionally equivalent and yet structurally unrelated to the pilotins found in <em>Klebsiella</em> and other bacteria. AspS binds to a specific targeting sequence in the <em>Vibrio</em>-type secretins, enhances the kinetics of secretin assembly, and homologs of AspS are found in all species of <em>Vibrio</em> as well those few strains of <em>Escherichia</em> and <em>Shigella</em> that have acquired a <em>Vibrio</em>-type T2SS.</p> </div>", "links"=>[], "tags"=>["ii", "secretion", "depends", "pilotin", "asps"], "article_id"=>114762, "categories"=>["Microbiology", "Biochemistry"], "users"=>["Rhys A. Dunstan", "Eva Heinz", "Lakshmi C. Wijeyewickrema", "Robert N. Pike", "Anthony W. Purcell", "Timothy J. Evans", "Judyta Praszkier", "Roy M. Robins-Browne", "Richard A. Strugnell", "Konstantin V. Korotkov", "Trevor Lithgow"], "doi"=>[nil, nil, nil, nil, nil, nil, nil, nil, nil], "stats"=>{"downloads"=>10, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Assembly_of_the_Type_II_Secretion_System_such_as_Found_in_em_Vibrio_cholerae_em_Depends_on_the_Novel_Pilotin_AspS/114762", "title"=>"Assembly of the Type II Secretion System such as Found in <em>Vibrio cholerae</em> Depends on the Novel Pilotin AspS", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-01-10 01:19:22"}

{"files"=>["https://ndownloader.figshare.com/files/510679"], "description"=>"<p>In <i>K. oxytoca</i>, PulD has three characterized domains: the N-domains (blue) that dock it to the inner membrane components of the T2SS, the secretin domain (pink) responsible for multimerization, and the C-terminal S-domain, which is critical for PulD to engage the pilotin PulS <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003117#ppat.1003117-Hardie1\" target=\"_blank\">[14]</a>–<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003117#ppat.1003117-Tosi1\" target=\"_blank\">[18]</a>. The predicted domain structure of GspD from EPEC is similarly shown, including the S-domain demonstrated to be necessary and sufficient for AspS binding. Also indicated are the T2SS secretins HxcQ and XcpQ from <i>Pseudomonas</i>, each of which has a C-terminal extension beyond the recognizable secretin domain which may or may not serve for binding of the protein of unknown function, PA3611.</p>", "links"=>[], "tags"=>["distinguished", "t2ss"], "article_id"=>181170, "categories"=>["Microbiology", "Biochemistry"], "users"=>["Rhys A. Dunstan", "Eva Heinz", "Lakshmi C. Wijeyewickrema", "Robert N. Pike", "Anthony W. Purcell", "Timothy J. Evans", "Judyta Praszkier", "Roy M. Robins-Browne", "Richard A. Strugnell", "Konstantin V. Korotkov", "Trevor Lithgow"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003117.g007", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Pilotins_distinguished_for_each_class_of_T2SS_secretin_/181170", "title"=>"Pilotins distinguished for each class of T2SS secretin.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-10 00:19:30"}

{"files"=>["https://ndownloader.figshare.com/files/509991"], "description"=>"<p>(A) The conserved domain architecture tool (CDART) was used to map the regions of PulS from <i>Klebsiella oxytoca</i> 10-5250 (EHT07154.1), OutS from <i>Dickeya dadantii</i> 3937 (YP_003883937.1), EtpO from Shiga toxin-producing <i>E. coli</i> (STEC) O157:H7 (CAA70966.1) and YacC (CAS07673.1) from EPEC. Numbers refer to the amino acids of each protein sequence, and the broken blue bar denotes that the N-terminal and C-terminal residues of YacC diverge from the consensus features of the PulS-OutS family. Pairwise sequence alignment over 80 residues showing similarity of the previously characterized EtpO (CAA70966.1) and YacC (CAS07673.1). Identical residues are highlighted between the two sequences, and conserved substitutions are shown (+). (B) CLANS analysis graphically depicts homology in large datasets of proteins, utilizing all-against-all pairwise BLAST to cluster representations (colored dots) of individual protein sequences in three-dimensional space. Lines are shown between the most similar sequences, with an E-value cut-off of 1e−5. The analysis shows that proteins from diverse species cluster into two groups: the PulS/OutS group and YacC-related proteins (blue), and the AspS-related proteins (red). There are numerous relationships between the PulS/OutS proteins and YacC proteins, but no relationship links these to the AspS group of proteins. (C) Wild-type EPEC (WT), and the indicated mutants of EPEC were grown in culture and post-cell supernatants containing secreted proteins (200 µg of protein) were analyzed by SDS-PAGE and Coomassie blue staining. Mass spectrometry was used to identify SslE, FliC and EspC, consistent with a previous study <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003117#ppat.1003117-Badea1\" target=\"_blank\">[72]</a>.</p>", "links"=>[], "tags"=>["puls-outs"], "article_id"=>180479, "categories"=>["Microbiology", "Biochemistry"], "users"=>["Rhys A. Dunstan", "Eva Heinz", "Lakshmi C. Wijeyewickrema", "Robert N. Pike", "Anthony W. Purcell", "Timothy J. Evans", "Judyta Praszkier", "Roy M. Robins-Browne", "Richard A. Strugnell", "Konstantin V. Korotkov", "Trevor Lithgow"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003117.g001", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/YacC_is_a_novel_member_of_the_PulS_OutS_family_of_proteins_/180479", "title"=>"YacC is a novel member of the PulS-OutS family of proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-10 00:07:59"}